6JWP: EGOC
crystal structure of EGOC. Determined by X-ray diffraction at 3.2 Å resolution. Released 11 Dec 2019.
- Method
- X-ray diffraction
- Resolution
- 3.2 Å
- Organism
- Saccharomyces cerevisiae S288c
- Chains
- 10
- Atoms
- 13,142
- Mol. weight
- 233.96 kDa
- Ligands
- GNP, MG
- Released
- 11 Dec 2019
Explore 6JWP in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6JWP contains 72 α-helices and 73 β-strands across 10 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 14 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 9-12 | 4 | 1 |
| α-helix | 19-26 | 8 | |
| α-helix | 34-37 | 4 | |
| α-helix | 38-42 | 5 | |
| β-strand | 45-51 | 7 | 1 |
| β-strand | 55-61 | 7 | 1 |
| α-helix | 66-72 | 7 | |
| α-helix | 77-80 | 4 | |
| β-strand | 87-92 | 6 | 1 |
| α-helix | 98-114 | 17 | |
| β-strand | 121-126 | 6 | 1 |
| α-helix | 133-136 | 4 | |
| α-helix | 137-151 | 15 | |
| β-strand | 160-164 | 5 | 1 |
| α-helix | 170-179 | 10 | |
| α-helix | 180-182 | 3 | |
| α-helix | 186-200 | 15 | |
| β-strand | 202-208 | 7 | 2 |
| β-strand | 215-218 | 4 | 2 |
| α-helix | 242-257 | 16 | |
| α-helix | 258-260 | 3 | |
| β-strand | 264-269 | 6 | 2 |
| β-strand | 273-276 | 4 | 2 |
| β-strand | 283-288 | 6 | 2 |
| α-helix | 295-306 | 12 | |
Chain B: 11 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 12-16 | 5 | 3 |
| α-helix | 22-31 | 10 | |
| α-helix | 36-39 | 4 | |
| β-strand | 48-52 | 5 | 3 |
| β-strand | 58-62 | 5 | 3 |
| α-helix | 76-80 | 5 | |
| β-strand | 85-91 | 7 | 3 |
| α-helix | 97-113 | 17 | |
| β-strand | 118-124 | 7 | 3 |
| α-helix | 131-150 | 20 | |
| β-strand | 161-164 | 4 | 3 |
| α-helix | 170-180 | 11 | |
| α-helix | 186-194 | 9 | |
| α-helix | 196-199 | 4 | |
| β-strand | 202-209 | 8 | 2 |
| β-strand | 215-217 | 3 | 2 |
| α-helix | 225-244 | 20 | |
| β-strand | 270-275 | 6 | 2 |
| β-strand | 280-285 | 6 | 2 |
| α-helix | 287-289 | 3 | |
| β-strand | 290-296 | 7 | 2 |
| α-helix | 303-322 | 20 | |
Chain C: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 44-70 | 27 | |
| α-helix | 74-79 | 6 | |
| β-strand | 83-85 | 3 | 4 |
| α-helix | 88-93 | 6 | |
| β-strand | 142-144 | 3 | 5 |
| α-helix | 147-149 | 3 | |
| α-helix | 154-170 | 17 | |
| β-strand | 181-182 | 2 | 6 |
Chain D: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 11-15 | 5 | 5 |
| β-strand | 21-26 | 6 | 5 |
| α-helix | 27-29 | 3 | |
| α-helix | 32-34 | 3 | |
| α-helix | 35-38 | 4 | |
| α-helix | 42-43 | 2 | |
| β-strand | 48-52 | 5 | 5 |
| β-strand | 56-63 | 8 | 5 |
| β-strand | 66-73 | 8 | 5 |
Chain E: 6 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-4 | 2 | 6 |
| α-helix | 6-15 | 10 | |
| β-strand | 21 | 1 | 7 |
| β-strand | 28 | 1 | 7 |
| α-helix | 30-32 | 3 | |
| β-strand | 34-39 | 6 | 4 |
| β-strand | 45-50 | 6 | 4 |
| α-helix | 65-84 | 20 | |
| β-strand | 95-100 | 6 | 4 |
| β-strand | 103-112 | 10 | 4 |
| β-strand | 115-121 | 7 | 4 |
| α-helix | 122 | 1 | |
| β-strand | 127-133 | 7 | 4 |
| α-helix | 139-150 | 12 | |
| α-helix | 154-156 | 3 | |
Chain F: 12 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-13 | 9 | 8 |
| α-helix | 19-27 | 9 | |
| α-helix | 34-37 | 4 | |
| α-helix | 39-42 | 4 | |
| β-strand | 44-47 | 4 | 8 |
| β-strand | 50-51 | 2 | 8 |
| β-strand | 55-62 | 8 | 8 |
| α-helix | 66-72 | 7 | |
| β-strand | 86-91 | 6 | 8 |
| α-helix | 98-114 | 17 | |
| β-strand | 120-126 | 7 | 8 |
| α-helix | 133-152 | 20 | |
| β-strand | 160-164 | 5 | 8 |
| α-helix | 170-180 | 11 | |
| α-helix | 186-200 | 15 | |
| β-strand | 202-208 | 7 | 9 |
| β-strand | 215 | 1 | 9 |
| α-helix | 242-254 | 13 | |
| α-helix | 257-260 | 4 | |
| β-strand | 264-269 | 6 | 9 |
| β-strand | 273-276 | 4 | 9 |
| β-strand | 283-288 | 6 | 9 |
| α-helix | 295-305 | 11 | |
| α-helix | 306-308 | 3 | |
Chain G: 7 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 21-27 | 7 | |
| α-helix | 96-98 | 3 | |
| α-helix | 173-182 | 10 | |
| α-helix | 186-199 | 14 | |
| β-strand | 202-209 | 8 | 9 |
| β-strand | 215-218 | 4 | 9 |
| α-helix | 225-245 | 21 | |
| α-helix | 249-251 | 3 | |
| β-strand | 270-275 | 6 | 9 |
| β-strand | 280-285 | 6 | 9 |
| β-strand | 290-296 | 7 | 9 |
| α-helix | 303-325 | 23 | |
Chain H: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-68 | 23 | |
| α-helix | 71-73 | 3 | |
| α-helix | 74-79 | 6 | |
| β-strand | 84 | 1 | 10 |
| α-helix | 88-93 | 6 | |
| β-strand | 142-143 | 2 | 11 |
| α-helix | 154-172 | 19 | |
| β-strand | 181-182 | 2 | 12 |
2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| GTP-binding protein GTR1 | A, F | protein | 312 | Saccharomyces cerevisiae S288c | Q00582 (AlphaFold model) |
| GTP-binding protein GTR2 | B, G | protein | 345 | Saccharomyces cerevisiae S288c | P53290 (AlphaFold model) |
| Protein MEH1 | C, H | protein | 129 | Saccharomyces cerevisiae S288c | Q02205 (AlphaFold model) |
| Ego2 | D, I | protein | 75 | Saccharomyces cerevisiae S288c | Q3E830 (AlphaFold model) |
| Protein SLM4 | E, J | protein | 162 | Saccharomyces cerevisiae S288c | P38247 |
Sequence of entity 1 (A, F), FASTA
>6JWP_1 GTP-binding protein GTR1 (chains A, F)
SHMSSNNRKKLLLMGRSGSGKSSMRSIIFSNYSAFDTRRLGATIDVEHSHLRFLGNMTLN
LWDCGGQDVFMENYFTKQKDHIFQMVQVLIHVFDVESTEVLKDIEIFAKALKQLRKYSPD
AKIFVLLHKMDLVQLDKREELFQIMMKNLSETSSEFGFPNLIGFPTSIWDESLYKAWSQI
VCSLIPNMSNHQSNLKKFKEIMNALEIILFERTTFLVICSSNGENSNENHDSSDNNNVLL
DPKRFEKISNIMKNFKQSCTKLKSGFKTLILNNNIYVSELSSNMVCFIVLKDMNIPQELV
LENIKKAKEFFQ
Sequence of entity 2 (B, G), FASTA
>6JWP_2 GTP-binding protein GTR2 (chains B, G)
MGIRMSLEATDSKAMVLLMGVRRCGKSSICKVVFHNMQPLDTLYLESTSNPSLEHFSTLI
DLAVMELPGQLNYFEPSYDSERLFKSVGALVYVIDSQDEYINAITNLAMIIEYAYKVNPS
INIEVLIHKVDGLSEDFKVDAQRDIMQRTGEELLELGLDGVQVSFYLTSIFDHSIYEAFS
RIVQKLIPELSFLENMLDNLIQHSKIEKAFLFDVNSKIYVSTDSNPVDIQMYEVCSEFID
VTIDLFDLYKAPVLRNSQKSSDKDNVINPRNELQNVSQLANGVIIYLRQMIRGLALVAII
RPNGTDMESCLTVADYNIDIFKKGLEDIWANARASQAKNSIEDDV
Sequence of entity 3 (C, H), FASTA
>6JWP_3 Protein MEH1 (chains C, H)
MANDEYDAEQMRLKEHEHEQKLLAREQELRDIVANTNDKLIDISMINNSGIVIQGTDLQE
ALDKRQPSSGSAQATTHQTAPRTNTFTLLTSPDSAKISKEQLKKLHSNILNEIFSQSQVN
KPGPLTVPF
Sequence of entity 4 (D, I), FASTA
>6JWP_4 Ego2 (chains D, I)
MEAEKQSDIKGTIAFDTHGNVIESTGVGSQRIEDIGDLSKVTLDAEGFAQVQGDSLLVHL
YKRNDITLAVYTSAQ
Sequence of entity 5 (E, J), FASTA
>6JWP_5 Protein SLM4 (chains E, J)
MVMLHSKNVKGFLENTLKPYDLHSVDFKTSSLQSSMIITATNGGILSYATSNNDVPKNSI
NEINSVNNLKMMSLLIKDKWSEDENDTEEQHSNSCYPVEIDSFKTKIYTYEMEDLHTCVA
QIPNSDLLLLFIAEGSFPYGLLVIKIERAMRELTDLFGYKLG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| GNP | Phosphoaminophosphonic acid-guanylate ester | C10 H17 N6 O13 P3 | 3 |
| MG | Magnesium ion | Mg | 3 |
Primary citation
Structural insights into the EGO-TC-mediated membrane tethering of the TORC1-regulatory Rag GTPases. Zhang, T., Peli-Gulli, M.P., Zhang, Z. et al. Sci Adv (2019) 5:eaax8164-eaax8164. DOI 10.1126/sciadv.aax8164 · PubMed
Other PDB entries of the same protein (UniProt Q00582 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3R7W 2.77 Å, Crystal Structure of Gtr1p-Gtr2p complex
- 4ARZ 3.1 Å, The crystal structure of Gtr1p-Gtr2p complexed with GTP-GDP
- 9H4Q 3.1 Å, Cryo-EM structure of the SEAC wing - EGOC
- 9H5K 3.2 Å, Cryo-EM structure of the SEAC-EGOC supercomplex
Browse structure collections
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